GWAS-extras + data files
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019244
OR
https://github.com/AAlhendi1707/GWAS
OR the updated version at
https://pbreheny.github.io/adv-gwas-tutorial/index.html
In the genome-wide association analysis section of the tutorial, you will get either a warning or an error about the genABEL package. Instead of loading genABEL, ignore the error/warning and source the functions ztransform, rntransform, estlambda and
GWAA.R (assuming those .R files are in your R working directory):
# Phenotype data preparation
# library(GenABEL)
source("ztransform.R")
source("rntransform.R")
source("estlambda.R")
source("GWAA.R")
NEW: If you are using R 4.0.x on a mac, you may get an error when you execute the GWAA function. If that happens, you should downgrade R to 3.6.0 (for example) and see if that works. If you still have problems, please contact me and we will try to work it out.